Transcription of Amber 12 Reference Manual
1 Amber 12 Reference Manual2 Amber 12 Reference ManualPrincipal contributors to the current codes:David A. Case (Rutgers University)Tom Darden (OpenEye)Thomas E. Cheatham III (Utah)Carlos Simmerling (Stony Brook)Junmei Wang (UT Southwestern Medical Center)Robert E. Duke (NIEHS and UNC-Chapel Hill)Ray Luo (UC Irvine)Ross C. Walker (SDSC, UCSD)Wei Zhang (UT Houston)Kenneth M. Merz (Florida)Benjamin P. Roberts (Florida)Seth Hayik (Florida)Adrian Roitberg (Florida)Gustavo Seabra (Recife, Brazil)Jason Swails (Florida)Andreas W. G tz (SDSC, UCSD)Istv n Kolossv ry (Budapest and Shaw)Kim F. Wong (Pitt)Francesco Paesani (UC San Diego)Jiri Vanicek (EPL-Lausanne)Romain M.
2 Wolf (Novartis)Jian Liu (Berkeley)Xiongwu Wu (NIH)Scott R. Brozell (Rutgers)Thomas Steinbrecher (Karlsruhe)Holger Gohlke (D sseldorf)Qin Cai (UC Irvine)Xiang Ye (UC Irvine)Jun Wang (UC Irvine)Meng-Juei Hsieh (UC Irvine)Guanglei Cui (Stony Brook)Daniel R. Roe (Rutgers University)David H. Mathews (Rochester)Matthew G. Seetin (Rochester)Romelia Salomon-Ferrer (SDSC, UCSD)Celeste Sagui (North Carolina State)Volodymyr Babin (North Carolina State)Tyler Luchko (Rutgers University)Sergey Gusarov (NINT)Andriy Kovalenko (NINT)Peter A. Kollman (UC San Francisco)Additional key contributors to earlier versions:David A. Pearlman (UC San Francisco)Robert V.
3 Stanton (UC San Francisco)Jed Pitera (UC San Francisco)Irina Massova (UC San Francisco)Ailan Cheng (Penn State)James J. Vincent (Penn State)Paul Beroza (Telik)Vickie Tsui (TSRI)Mike Crowley (NREL)John Mongan (UC San Diego)Bing Wang (Florida)Chunhu Tan (UC Irvine)Lijiang Yang (UC Irvine)Christian Schafmeister (Pitt)Wilson S. Ross (UC San Francisco)Randall Radmer (UC San Francisco)George L. Seibel (UC San Francisco)James W. Caldwell (UC San Francisco)U. Chandra Singh (UC San Francisco)Paul Weiner (UC San Francisco)For more information, please support from DARPA, NIH and NSF for Peter Kollman is gratefully acknowledged,as is support from NIH, NSF, ONR and DOE for David Case.
4 Use of the facilities of the UCSFC omputer Graphics Laboratory (Thomas Ferrin, PI) is appreciated. The pseudocontact shiftcode was provided by Ivano Bertini of the University of Florence. We thank Chris Bayly andMerck-Frosst, Canada for permission to include charge increments for the AM1-BCC chargescheme. Many people helped add features to various codes; these contributions are described inthe documentation for the individual programs; see also Citations: When citing Amber 12 in the literature, the following citation should be Case, Darden, Cheatham, III, Simmerling, J. Wang, Duke, , Walker, W.
5 Zhang, Merz, B. Roberts, S. Hayik, A. Roitberg, G. Seabra,J. Swails, G tz, I. Kolossv ry, Wong, F. Paesani, J. Vanicek, Wolf, J. Liu,X. Wu, Brozell, T. Steinbrecher, H. Gohlke, Q. Cai, X. Ye, J. Wang, Hsieh, , Roe, Mathews, Seetin, R. Salomon-Ferrer, C. Sagui, V. Babin, , S. Gusarov, A. Kovalenko, and Kollman (2012), Amber 12, University ofCalifornia, San history of the codes and a basic description of the methods can be found in three papers: Pearlman, Case, Caldwell, Ross, Cheatham, III, S. DeBolt,D. Ferguson, G. Seibel, and P. Kollman. Amber , a package of computer programs forapplying molecular mechanics, normal mode analysis, molecular dynamics and free en-ergy calculations to simulate the structural and energetic properties of ,1-41 (1995).
6 Case, T. Cheatham, T. Darden, H. Gohlke, R. Luo, Merz, Jr., A. Onufriev, , B. Wang and R. Woods. The Amber biomolecular simulation ,1668-1688 (2005). R. Salomon-Ferrer, Case, R. C Walker. An overview of the Amber BiomolecularSimulation Comput. Mol. press (2012).Peter Kollman died unexpectedly in May, 2001. We dedicate Amber to his IllustrationThe cover image represents the allosteric changes in the transcriptional repressor proteinStaphylococcus aureusCzrA upon binding of Zn(II). As Zn(II) binds DNA bound apo-CzrA(upper right image) the DNA binding affinity is reduced by 4 orders of magnitude and the struc-ture of CzrA switches from a + closed conformation to an open conformation facilitatingits release from DNA (lower left image).
7 See created by M. Nihan Ucisik, Dhruva Chakravorty and Kenneth M. Merz, to read next .. of Amber 12 .. tutorials ..102 Sander .. usage .. input files .. of the information in the input file .. minimization and dynamics parameters .. flags describing the calculation .. and format of the input .. and format of the output .. or restrained atoms .. minimization .. dynamics .. regulation .. regulation .. bond length constraints .. Water cap .. NMR refinement options .. EMAP constraints .. function parameters .. parameters .. Mesh Ewald .. IPS for the calculation of nonbonded interactions.
8 Point options .. potentials .. Printing .. MPI Timings .. conditions .. redirection commands .. debugging information ..423 CONTENTS3 Force field Generalized Born/Surface Area Model .. input parameters .. (Analytical Linearized Poisson-Boltzmann) .. Interaction Site Model of Molecular Solvation .. Time Step Methods for 3D-RISM .. insander.. Valence Bond .. usage description .. sampling .. of nuclear degrees of freedom .. Gaussian EVB .. input variables and interdependencies .. AMOEBA force field .. calculations: Semi-empirical methods .. hybrid QM/MM potential.
9 QM/MM interface and link atoms .. reformulated QM/MM interface for PM3 .. Born implicit solvent .. and PME .. for running successful QM/MM calculations .. QM/MM &qmmm Namelist Variables .. Atom Specific QM/MM &qmmm Namelist Variables .. calculations:ab initioand DFT methods .. Remarks .. Considerations .. Relocation .. Input Files for Charge Relocation .. 1074 Sampling and free integration .. inputs for thermodynamic integration .. Potentials in Thermodynamic Integration .. potential energy differences for FEP calculations .. sampling .. Langevin dynamics.
10 MD .. MD (MTMD) .. in the &tgt namelist:.. Molecular Dynamics (SMD) and the Jarzynski Relationship .. and usage .. Exchange Molecular Dynamics (REMD) .. REMD simulations .. REMD simulations .. of the output files .. changes from sander when using replica exchange .. when using replica exchange .. exchange example .. exchange using a hybrid solvent model .. REMD .. replica exchange .. RXSGLD: Replica exchange using Self-Guided Langevin Dynamics .. biased MD, steered MD, and umbrella sampling with REMD .. Coordinates.
